Silicone is wonderful stuff for many applications but, IMHO, this isn't one of them. Its consistency and curing rate make it kind of a pain to work with in many applications. Your examples are two of my favorites. For these, plumber's putty works so well, lasts so long (like indefinitely), is so easy to work with and is so forgiving of errors there's really no contest.

Silicone works real well 20' deep in a land fill, un-opened.

OK. I removed the entire drain step... cleaned the area of the silicone, applied putty, reassembled... and still a little drip leak from between the nut and the threads. It seems like this is coming from the water that goes down the drain, and between the drain stem and the sink... so, what is going wrong here that it is leaking on the threads... no leak between the sink and the tapered rubber fitting or between the nut and the rubber fitting... it is between the nut and the threads it is on. Is the rubber ring also supposed to seal this? I have tried it from snug to extremely tight... and no difference. Any suggestions?

Did you truly get all the silicone off?

I konw that the times I've had to remove it, it's a bear to get completely gone. and other stuff doesn't stick to it.